X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=86a1100c909cad066b4cef2378e6deb28cce5b4c;hb=51a7eedfc7d55c6f2dae8a75dcda6c4ccbe81893;hp=25fc04bd396a1db701d3b2de658acb538b6cfe85;hpb=5dd91255a15114eacfaa0122c12462cde592ce86;p=jalview.git
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@@ -71,32 +71,83 @@ li:before {
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General
- More robust colours and shader model for alignments and groups
- - Custom BLOSUM/Clustal type shading schemes can be created via groovy scripts
-
- - Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!)
+
- Custom shading schemes created via groovy scripts
+ - linked scrolling of CDS/Protein views via Overview or sequence motif search operations
+ - Efficiency improvements for interacting with alignment and overview windows
+ - Hidden columns and sequences can be omitted in Overview
+ -
+ Posterior probability annotation from
+ Stockholm files imported as sequence associated annotation
+
+ -
+ Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+
+ - Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
+ - Graduated feature colour style example included in the example feature file
Application
-
+ -
+
+ Experimental Features Checkbox in Desktop's Tools
+ menu to hide or show untested features in the application.
+
+ - Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
- Faster Chimera/Jalview communication by file-based command exchange
- URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
-
+ - Updated JABAWS client to v2.2
+
+ Experimental features
+
+ -
+ New entries in the Chimera menu
+ to transfer Chimera's structure attributes as Jalview
+ features, and vice-versa.
+
Applet
+ Test Suite
+ Added PrivilegedAccessor to test suite
+ Prevent or clear modal dialogs raised during tests
+
+
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General
- - Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
+ -
+ Fixed incorrect value in BLOSUM 62 score
+ matrix - C->R should be '-3'
Old matrix restored with
+ this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+
+ -
+ Fixed Jalview's treatment of gaps in PCA
+ and substitution matrix based Tree calculations.
In
+ earlier versions of Jalview, gaps matching gaps were
+ penalised, and gaps matching non-gaps penalised even more.
+ In the PCA calculation, gaps were actually treated as
+ non-gaps - so different costs were applied, which meant
+ Jalview's PCAs were different to those produced by
+ SeqSpace.
Jalview now treats gaps in the same way as
+ SeqSpace (ie it scores them as 0). To restore pre-2.10.2
+ behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
+ 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
+ restore 2.10.2 mode
+
+ - Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
- Hidden regions in alignment views are not coloured in linked structure views
- Current selection lost if popup menu opened on a region of alignment without groups
- Popup menu not always shown for regions of an alignment with overlapping groups
@@ -108,6 +159,18 @@ li:before {
- Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
- Protein specific colours only offered in colour and group colour menu for protein alignments
- 'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
+ - Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
+ - Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
+ - Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
+ - Sequence features shown in tooltip for gaps before start of features
+ - Very large alignments take a long time to load
+ - Graduated feature colour threshold not restored to UI when feature colour is edited
+ - Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%
+ - Structure and alignment overview update as graduate feature colour settings are modified via the dialog box
+ - Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.
+ - Overview window doesn't always update when a group defined on the alignment is resized
+ - Mouseovers on left/right scale region in wrapped view result in positional status updates
+ - Status bar shows position for ambiguous amino acid and nucleotide symbols
Application
@@ -120,17 +183,29 @@ li:before {
- Typo in selection popup menu - Create groups now 'Create Group'
- CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
- Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
- - DAS registry not found exceptions removed from console output
-
+ - DAS registry not found exceptions removed from console output
+ - Above PID colour threshold not recovered when alignment view imported from project
+ - No mappings generated between structure and sequences extracted from structure files imported via URL
+ -
+ Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+
+ - Trackpad horizontal scroll gesture adjusts start position in wrap mode
+ - Status bar doesn't show positions for ambiguous amino acids
+ - Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns
Applet
- Features not rendered as transparent on overview or linked structure view
- Colour group by conservation doesn't work (since 2.8)
+ - Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme
New Known Issues
-
+ - Protein/CDS view scrolling not always in phase after a sequence motif find operation
+ - Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols
+ - Cannot load Newick trees from eggnog ortholog database
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